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cisevol fungi [28 articles]

Recent papers added to cisevol library classified by the tag fungi. You can also see everyone's fungi.
  • The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model.
    EMBO reports, Vol. 5, No. 3. (March 2004), pp. 280-284.
    by V van Noort, B Snel, MA Huynen
    posted to fungi expression duplication by cisevol on 2008-07-23 09:01:02 as ** along with 1 group cis-regulatory-evolution
  • Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.
    Nucleic Acids Res, Vol. 32, No. 16. (2004), pp. 4725-4731.
    by B Snel, V van Noort, MA Huynen
    posted to worms fungi expression duplication bacteria by cisevol on 2008-07-23 09:00:05 as ** along with 1 person and 1 group bjorns cis-regulatory-evolution
  • Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
    Nature, Vol. 440, No. 7082., pp. 341-345.
    by Devin R Scannell, Kevin P Byrne, Jonathan L Gordon, Simon Wong, Kenneth H Wolfe
    posted to fungi duplication by cisevol on 2008-07-22 20:22:48 as ** along with 5 people and 2 groups RMGraze dpollard cmm echinotrix souravc EisenLab FAB-lab
  • Functional Analysis of Gene Duplications in Saccharomyces cerevisiae
    Genetics, Vol. 175, No. 2. (1 February 2007), pp. 933-943.
    by Yuanfang Guan, Maitreya J Dunham, Olga G Troyanskaya
    posted to fungi duplication cis-regulatory by cisevol on 2008-07-22 20:17:40 as ** along with 3 people and 1 group carlk TaqSys csaveanu cis-regulatory-evolution
  • Retrotransposon Tf1 is targeted to Pol II promoters by transcription activators.
    Molecular cell, Vol. 30, No. 1. (11 April 2008), pp. 98-107.
    by YE Leem, TL Ripmaster, FD Kelly, H Ebina, ME Heincelman, K Zhang, SI Grewal, CS Hoffman, HL Levin
    posted to fungi expression cis-regulatory by cisevol on 2008-05-10 09:06:08 as ** along with 2 groups cis-regulatory-evolution BergmanLab
  • Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs.
    J Mol Biol, Vol. 158, No. 4. (15 July 1982), pp. 573-597.
    by T Ikemura
    posted to fungi codon_bias by cisevol on 2008-04-25 12:49:50 as ** along with 1 person and 1 group bjorns BergmanLab
  • Genetic Properties Influencing the Evolvability of Gene Expression.
    Science (24 May 2007)
    by Christian R R Landry, Bernardo Lemos, Scott A A Rifkin, W J J Dickinson, Daniel L L Hartl
    posted to cis-regulatory fungi microarray by cisevol on 2008-02-18 19:22:19 as ** along with 10 people and 3 groups klo jjray brant balicea sebastien_vigneau grahamc emarker heliopais caseybrown emptyhb EisenLab ParkinsonLab_at_MaRS cis-regulatory-evolution
  • On the relation between promoter divergence and gene expression evolution
    Mol Syst Biol, Vol. 4 (15 January 2008)
    by Itay Tirosh, Adina Weinberger, Dana Bezalel, Mark Kaganovich, Naama Barkai
    posted to cis-regulatory fungi microarray by cisevol on 2008-01-30 20:35:13 as ** along with 8 people and 2 groups Jporci balicea kengg zwang biomcgary caseybrown renatomilani mclarenv cis-regulatory-evolution BergmanLab
  • Evolution of alternative transcriptional circuits with identical logic
    Nature, Vol. 443, No. 7110. (2006), pp. 415-420.
    by Annie E Tsong, Brian B Tuch, Hao Li, Alexander D Johnson
    posted to cis-regulatory fungi by cisevol on 2008-01-12 15:13:22 as ** along with 6 people and 4 groups emptyhb marcius brant adepace aswin srfairclough EisenLab BioinfoCIPF SGU-CIPF cis-regulatory-evolution
  • Evolution of a combinatorial transcriptional circuit: a case study in yeasts.
    Cell, Vol. 115, No. 4. (14 November 2003), pp. 389-399.
    by AE Tsong, MG Miller, RM Raisner, AD Johnson
    posted to cis-regulatory fungi by cisevol on 2008-01-12 15:12:46 as ** along with 1 group cis-regulatory-evolution
  • Transcriptional cosuppression of yeast Ty1 retrotransposons.
    Genes Dev, Vol. 16, No. 4. (15 February 2002), pp. 467-478.
    by YW Jiang
    posted to fungi transposon by cisevol on 2007-12-10 23:12:53 as ** along with 1 group BergmanLab
  • Genome-wide regulatory complexity in yeast promoters: Separation of functionally conserved and neutral sequence.
    Genome Res, Vol. 15, No. 2. (February 2005), pp. 205-213.
    by CS Chin, JH Chuang, H Li
    posted to cis-regulatory fungi by cisevol on 2007-10-24 17:56:37 as ** along with 3 people and 1 group briann lusk nklee cis-regulatory-evolution
  • Genomic Evolution of the Proteasome System Among Hemiascomycetous Yeasts.
    J Mol Evol (2 October 2007)
    by Gertrud Mannhaupt, Horst Feldmann
    posted to cis-regulatory fungi by cisevol on 2007-10-21 19:16:27 as ** along with 1 group cis-regulatory-evolution
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to cis-regulatory fungi by cisevol on 2007-10-19 15:33:26 as ** along with 24 people and 8 groups aalibes snow_dragon kristallreiner mariakmejia brant alokm tuck chad_davis lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • Genetic interactions between polymorphisms that affect gene expression in yeast
    Nature, Vol. 436, No. 7051., pp. 701-703.
    by Rachel B Brem, John D Storey, Jacqueline Whittle, Leonid Kruglyak
    posted to cis-regulatory fungi variation by cisevol on 2007-10-17 21:42:07 as ** along with 3 people and 3 groups mrockman JAShapiro dpollard RockmanLab EisenLab cis-regulatory-evolution
  • Comparative analysis indicates regulatory neofunctionalization of yeast duplicates
    Genome Biology, Vol. 8 (05 April 2007), R50.
    by Itay Tirosh, Naama Barkai
    posted to cis-regulatory duplication fungi by cisevol on 2007-10-17 21:38:17 as ** along with 3 people and 2 groups adepace stajich ajpowell EisenLab cis-regulatory-evolution
  • Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors.
    Genome Res (5 July 2007)
    by Daryi Wang, Huang-Mo M Sung, Tzi-Yuan Y Wang, Chih-Jen J Huang, Peggy Yang, Tiffany Chang, Yang-Chao C Wang, Da-Lun L Tseng, Jen-Pey P Wu, Tso-Ching C Lee, Ming-Che C Shih, Wen-Hsiung H Li
    posted to cis-regulatory fungi by cisevol on 2007-10-17 20:55:12 as ** along with 4 people and 3 groups emptyhb dpollard jwestbrook emarker EisenLab King_Lab cis-regulatory-evolution
  • Divergence of Transcription Factor Binding Sites Across Related Yeast Species
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819.
    by Anthony R Borneman, Tara A Gianoulis, Zhengdong D Zhang, Haiyuan Yu, Joel Rozowsky, Michael R Seringhaus, Lu Y Wang, Mark Gerstein, Michael Snyder
    posted to cis-regulatory fungi by cisevol on 2007-10-17 20:37:02 as ** along with 16 people and 2 groups anka nklee aalibes chad_davis dpollard djkt mikaelhuss lusk cjeans sujaikumar zwang GustavoLacerda Jporci maximilianh njcitulike emptyhb EisenLab cis-regulatory-evolution
  • The Role of Cis-Regulatory Motifs and Genetical Control of Expression in the Divergence of Yeast Duplicate Genes.
    Mol Biol Evol (10 September 2007)
    by Lindsey J J Leach, Ze Zhang, Chenqi Q Q Lu, Michael J J Kearsey, Zewei W W Luo
    posted to cis-regulatory fungi by cisevol on 2007-10-17 08:47:32 as ** along with 1 person and 2 groups brant EisenLab cis-regulatory-evolution
  • Position specific variation in the rate of evolution in transcription factor binding sites.
    BMC Evol Biol, Vol. 3, No. 1. (28 August 2003)
    by AM Moses, DY Chiang, M Kellis, ES Lander, MB Eisen
    posted to cis-regulatory fungi model by cisevol on 2007-10-16 22:54:28 as ** along with 6 people and 2 groups emptyhb briann dpollard adepace lusk nklee EisenLab cis-regulatory-evolution
  • MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
    Genome Biol, Vol. 5, No. 12. (2004)
    by AM Moses, DY Chiang, DA Pollard, VN Iyer, MB Eisen
    posted to cis-regulatory fungi model by cisevol on 2007-10-16 22:54:15 as ** along with 5 people and 2 groups ihpark tuck indigoviolet lusk Garamonfok EisenLab cis-regulatory-evolution
  • Sequencing and comparison of yeast species to identify genes and regulatory elements.
    Nature, Vol. 423, No. 6937. (15 May 2003), pp. 241-254.
    by M Kellis, N Patterson, M Endrizzi, B Birren, ES Lander
    posted to cis-regulatory fungi by cisevol on 2007-10-16 22:42:56 as ** along with 8 people and 4 groups evaf RMGraze balajis opheliav dchughes dquest franklin azazello G4ID Genetics-of-Gambling MBLAB cis-regulatory-evolution
  • Phylogeny based discovery of regulatory elements.
    BMC Bioinformatics, Vol. 7 (2006)
    by J Gertz, JC Fay, BA Cohen
    posted to cis-regulatory fungi model by cisevol on 2007-10-16 22:32:39 as ** along with 2 people and 2 groups indigoviolet dquest EisenLab cis-regulatory-evolution
  • Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi.
    PLoS Biol, Vol. 2, No. 12. (9 November 2004)
    by Audrey P P Gasch, Alan M M Moses, Derek Y Y Chiang, Hunter B B Fraser, Mark Berardini, Michael B B Eisen
    posted to cis-regulatory fungi by cisevol on 2007-10-16 22:32:13 as ** along with 4 people and 3 groups mbeisen tsackton nickluscombe lusk EisenLab EBI-regulation cis-regulatory-evolution
  • Identification of functional transcription factor binding sites using closely related Saccharomyces species.
    Genome Res, Vol. 15, No. 5. (May 2005), pp. 701-709.
    by SW Doniger, J Huh, JC Fay
    posted to cis-regulatory fungi by cisevol on 2007-10-16 22:14:04 as ** along with 1 group cis-regulatory-evolution
  • Frequent Gain and Loss of Functional Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e99.
    by Scott W Doniger, Justin C Fay
    posted to cis-regulatory fungi model by cisevol on 2007-10-16 22:13:42 as ** along with 7 people and 2 groups emptyhb brant dpollard sebastien_vigneau zwang maximilianh xili03 EisenLab cis-regulatory-evolution
  • Finding functional features in Saccharomyces genomes by phylogenetic footprinting.
    Science, Vol. 301, No. 5629. (4 July 2003), pp. 71-76.
    by P Cliften, P Sudarsanam, A Desikan, L Fulton, B Fulton, J Majors, R Waterston, BA Cohen, M Johnston
    posted to cis-regulatory fungi by cisevol on 2007-10-16 22:10:59 as ** along with 4 people and 1 group evaf chad_davis dquest Eonwe cis-regulatory-evolution
  • Rate of promoter class turn-over in yeast evolution.
    BMC Evol Biol, Vol. 6 (2006)
    by GA Bazykin, AS Kondrashov
    posted to cis-regulatory fungi by cisevol on 2007-10-16 22:04:38 as ** along with 1 group cis-regulatory-evolution
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